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首页> 外文期刊>Journal of Molecular Biology >An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence.
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An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence.

机译：蛋白质序列和结构分析和建模的综合方法。二。关于序列之间没有明显关联的蛋白质的序列与结构相似性之间的关系。

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摘要

Here, we discuss the relationship between protein sequence and protein structural similarity. It is established that a protein structural distance (PSD) of 2.0 is a threshold above which two proteins are unlikely to have a detectable pairwise sequence relationship. A precise correlation is established between the level of sequence similarity, defined by a normalized Smith-Waterman score, and the probability that two proteins will have a similar structure (defined by pairwise PSD<2). This correlation can be used in evaluating the likelihood for success in a comparative modeling procedure. We establish the existence of a correlation between sequence and structural similarity for pairs of proteins that are related in structure but whose sequence relationship is not detectable using standard pairwise sequence alignments. Although it is well known that there is a close relationship between sequence and structural similarity for pairwise sequence identities greater than about 30 %, there has been little discussion as to the possible existence of such a relationship for pairs of proteins in or below the twilight zone of sequence similarity (<25 % pairwise sequence identity). Possible implications of our results for the evolution of protein structure are discussed. Copyright 2000 Academic Press.
机译：在这里，我们讨论蛋白质序列和蛋白质结构相似性之间的关系。已确定蛋白质结构距离（PSD）为2.0是一个阈值，在该阈值之上，两种蛋白质不太可能具有可检测的成对序列关系。在由标准化Smith-Waterman分数定义的序列相似性水平与两种蛋白质具有相似结构的可能性（由成对PSD <2）之间建立了精确的相关性。此相关性可用于评估比较建模过程中成功的可能性。我们建立了结构与蛋白质对之间的序列和结构相似性之间相关性的存在，但使用标准的成对序列比对无法检测到其序列关系。尽管众所周知，成对的序列同一性大于约30％时，序列和结构相似性之间存在密切的关系，但关于微区中或以下的蛋白质对可能存在这种关系的讨论很少序列相似性（小于25％的成对序列同一性）。讨论了我们的结果可能对蛋白质结构演变的影响。版权所有2000学术出版社。

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